A stool transplant delivers billions of microbes into a sick gut. Almost none move in for good. We followed donor-recipient pairs from whole communities down to single nucleotides, and found the gut runs a ruthless strain-level filter. Out now in Cell Reports 🧵 www.cell.com/cell-reports...

Strain-level ecological filtering governs microbial colonization of the human gut

Baertschi et al. demonstrate that microbiota transplantation functions as a selective ecological filter. Although donor species frequently appear, only specific lineages achieve stable strain integrat...

cell.com

Universität Bern@unibe.ch · 2d ago

A strict “gatekeeper” decides whether a #fecaltransplant is effective: sohub.io/wruy. This is shown by a new study led by @bahtiyil.bsky.social from #unibern & @inselgruppe.bsky.social @dbmr-unibe.bsky.social

Session proposals are now open for ASM Microbe 2027 ! asm.org/events/asm-m... If there is a specific topic or speaker you would like to see in Chicago, this is your chance (until Aug 12) ! This is for Micro Symposia and Hub Sessions, but my DMs are open if you have ideas for bigger AEM sessions

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature

Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.

go.nature.com

New work led by @stevenjrobbins.bsky.social @markoterzin.bsky.social finally published - we now have a reference of microbial genomic resources from the Great Barrier Reef. The paper came out just hours after the work presented by Marko at #ICRS2026 @icrs.bsky.social See thread here for more detail

Steven Robbins@stevenjrobbins.bsky.social · 2w ago

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

Leveraging the GBR-MGD, we find that seawater microbes reflect and are predictive of the impacts of reef management strategies. However, there's a lot more work to be done to determine why and how this occurs. bsky.app/profile/stev...

Steven Robbins@stevenjrobbins.bsky.social · 2w ago

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

In addition to GC and strain bias, certain taxa showed systematically underestimated completeness via CheckM1 and 2, so historically much more likely to get erroneously thrown away in fragmented short read MAGs—a 3rd reason for the existence of Ghost Taxa. A sub-🧵. bsky.app/profile/stev...

Steven Robbins@stevenjrobbins.bsky.social · 2w ago

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

For 10+ years, short reads left the ocean's most dominant microbes unstudied. Now we can finally see them. Steven & the team used nanopore reads to assemble the ocean's most abundant "Ghost Taxa." The microbes, invisible for a decade, could also reflect the condition of the reef around them. #WYMM

Steven Robbins@stevenjrobbins.bsky.social · 2w ago

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

Short-read metagenomic sequencing cannot recover genomes from many abundant marine prokaryotes due to high strain heterogeneity and platform-specific GC bias (likely viruses, too), but Nanopore long reads can address this. A results 🧵on our recent paper in @nature.com . bsky.app/profile/stev...

Steven Robbins@stevenjrobbins.bsky.social · 2w ago

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂 www.nature.com/articles/s41...

The planktonic microbiome of the Great Barrier Reef - Nature

The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...

nature.com

my first 'data descriptor'! hoping this one will be useful for folks interested in tracing the distribution of genomes/genes/proteins over physicochemical gradients in the (deep) marine water column.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w ago

Deeply-sequenced metagenomes and over 1000 draft genomes from the epipelagic to bathypelagic Northeast Pacific Ocean https://www.biorxiv.org/content/10.64898/2026.07.18.739368v1

We have a bunch of MAGs sitting in GenBank queues for many months. I run all MAGs through PGAP so they’re BLAST-able & assigned accessions, which I refer to when discussing genes in MAGs in papers. This has ground to a halt w/ NCBI processing delays in recent years. Is there anyway to expedite this?

Predicting oxygen levels in microbial habitats using a metagenome-based approach #microbiology #metagenomics #oxygen @asm.org doi.org/10.1128/msys...

Predicting oxygen levels in microbial habitats using a metagenome-based approach | mSystems

Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.

doi.org

Restriction-site-based enrichment coupled to adaptive sampling enables long-read transposon-insertion sequencing https://www.biorxiv.org/content/10.64898/2026.06.23.733934v1

I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬

Follow-up to my last blog post: I now look at assembly polishing with Dorado v2 and the new hac@v6.0.0 model from @nanoporetech.com. rrwick.github.io/2026/06/19/d...

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

For anyone doing ONT Microbial Genomics, please take 1 minute (less?) to tell us which assembly metrics you care most about when evaluating whether an assembly is "good". We are doing a benchmark of different QC tools (barcode/adapter trimming and QC filtering). microbial-qc-survey.streamlit.app

Microbial QC Survey

A standalone Streamlit app that collects community priority weights over fourassembly-QC metrics ...

microbial-qc-survey.streamlit.app

Is @nanoporetech.com hac v6 better than 5.2.0 sup? The short answer is no. But are a few errors in a genome worth 5 times more basecalling compute? github.com/Kirk3gaard/M...

New blog post! I analyse the new hac@v6.0.0 basecalling model from @nanoporetech.com and discuss the conspicuous lack of a new sup model: rrwick.github.io/2026/06/11/d...

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis - The Lancet Microbe www.thelancet.com/journals/lan... #microsky

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis

These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to cl...

thelancet.com

The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods

The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

nature.com

My solar panels produced more electricity than I used this month. Eat my SHORTS climate change.

Thought i'd highlight that the ONT London Calling tech talk is now up. Points of interest for the microbiome community: 1) Direct RNA multiplexing now available. Can now run 24 samples per flow cell, recover full-length transcripts with 8 base pair modifications... www.youtube.com/watch?v=CE69...

London Calling 2026 Technology update

YouTube video by Oxford Nanopore Technologies

youtube.com

On real 16S ONT amplicon data, savont gets a lot more diversity and ASVs compared to existing methods. But these aren't just false positives. The dataset (from @mkddueholm.bsky.social and team) had paired PacBio HiFi data as a orthogonal reference: ~98% of the ONT ASVs mapped perfectly. 5/6

For long 16S nanopore amplicons (R10.4, sup-basecalled), savont requires 5-16x less depth for capturing ASVs. This improvement is more stark for longer amplicons (e.g. rRNA operon). For HiFi, savont + existing ASV methods are comparable, although savont misses a few intragenomic 16S copies. 4/6

Savont instead uses a high-resolution clustering approach: cluster similar reads --> create an error-free consensus. The problem is resolving clusters at the single nucleotide level to get true ASVs. To do this, we adopted the "SNPmer" technique: cluster reads by their polymorphic k-mers. 3/6

Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2mo ago

Sensitive long-read amplicon sequence variant recovery with savont https://www.biorxiv.org/content/10.64898/2026.05.26.727271v1

For many years you needed UMIs and similar dark molecular biology magic to get perfect amplicon sequences from @nanoporetech.com data. With recent accuracy improvements+really clever algorithms that is now changed. Savont unlocks ASVs from low coverage nanopore amplicon data 🤯🤯🤯

Jim Shaw@jimshaw.bsky.social · 2mo ago

Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

Between making ONT ASVs possible (Savont), meaningfully improving metagenomic assembly (Myloasm), and highly accurate metagenimic taxonomic profiling (Sylph), @jimshaw.bsky.social is kicking goals lately.

Christine He@christinehe.bsky.social · 2mo ago

Come to ONT's industry event at ASM to hear about two exciting new tools from @jimshaw.bsky.social! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇

Come to ONT's industry event at ASM to hear about two exciting new tools from @jimshaw.bsky.social! SNPmers (polymorphic kmers) are leveraged for impressive performance in both myloasm (metagenomic assembly) and savont (16S ASVs). Registration link 👇

Oxford Nanopore@nanoporetech.com · 2mo ago

Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. https://bit.ly/4v4XuKE